Computational fluid dynamics (CFD) have been playing an increasingly important role in designing the agriculture control environment structure in the past few years. Plant factory is a fully enclose control environment agriculture structure developed to create optimum growing conditions for the crops. Previous studies have proven that the CFD technique was able to analyse and predict the internal climate of the plant factory in the designing stage before the actual plant was built. This study was conducted to analyse the changes in airflow characteristics and temperature distribution in a shipping container size plant factory with different inlet and outlet locations. Uniformity of airflow and temperature distribution was important in plant factories as it is responsible to create optimum and uniform growing conditions for crops. The CFD model was validated by comparing simulation and experimental data of existing plant factory inlet and outlet location. The validation result shows an acceptable percentage error between simulated and measured data. Two alternative design of the inlet and outlet location was simulated to improve the uniformity of airflow and temperature distribution. The validated CFD model was then used to simulate the alternative design. Finally, the location of the inlet and the outlet that produce the most uniform airflow and temperature distribution inside the plant factory was identified.